genomeplot {nplplot} | R Documentation |
Creation of Genome Graph files
Description
The genomeplot
function generates two formatted files, one
containing “chromosome base” formatted genome data and the other
containing marker-specific results with dbSNP SNP IDs for displaying
genome-wide data sets in the UCSC genome browser.
Usage
genomeplot(gg.data)
Arguments
gg.data |
a file containing chromosome, marker, physical position and scores. |
Details
gg.data example:
Chromosome Marker Position TRAIT_ALL 5 M1 0.000 0.670 5 - 2.500 0.640 5 M3 5.000 0.590 5 - 6.500 0.600 5 M2 8.000 0.610 8 M4 0.000 0.670 8 - 2.500 0.640 8 M6 5.000 0.590 8 - 6.500 0.600 8 M5 8.000 0.610
Two files are created, “GG.positons.all” for the
“chromosome base” format, and “GG.markers.all” for the
marker-names based format. When there are multiple scores in
gg.data
file, this results in matched pairs of files, one for
each score, labelled with the score names, e.g. GG.positions.score1.all,
and GG.markers.score1.all, GG.positions.score2.all and
GG.markers.score2.all, and so on.
Value
TRUE or FALSE depending on whether runs successfully.
Examples
## Not run: genomeplot("GG.data.all")